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- PDB-7ze0: Solution structure of the PulM C-terminal domain from Klebsiella ... -

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Basic information

Entry
Database: PDB / ID: 7ze0
TitleSolution structure of the PulM C-terminal domain from Klebsiella oxytoca
ComponentsType II secretion system protein M
KeywordsPROTEIN TRANSPORT / Klebsiella oxytoca T2SS GENERAL SECRETION PATHWAY Ferredoxin-like domain
Function / homology:
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsLopez-Castilla, A. / Bardiaux, B. / Nilges, M. / Francetic, O. / Izadi-Pruneyre, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-14-CE09-0004 France
CitationJournal: Structure / Year: 2023
Title: Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system.
Authors: Dazzoni, R. / Li, Y. / Lopez-Castilla, A. / Brier, S. / Mechaly, A. / Cordier, F. / Haouz, A. / Nilges, M. / Francetic, O. / Bardiaux, B. / Izadi-Pruneyre, N.
History
DepositionMar 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II secretion system protein M
B: Type II secretion system protein M


Theoretical massNumber of molelcules
Total (without water)17,8762
Polymers17,8762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, mass spectrometry, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Type II secretion system protein M / T2SS protein M / General secretion pathway protein M


Mass: 8938.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The S79 comes from the TEV cleavage / Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DVB85_16620 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B2TA77

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HMQC
131isotropic23D CBCA(CO)NH
1171isotropic23D HN(CA)CB
151isotropic23D C(CO)NH
1101isotropic23D HNCO
1181isotropic23D HN(CA)CO
161isotropic23D H(CCO)NH
1121isotropic23D 1H-15N NOESY
1111isotropic23D 1H-13C NOESY
1152isotropic23D 13C/15N-filtered NOESY
1161isotropic22D (HB)CB(CGCD)HD
1191isotropic22D (HB)CB(CGCDCE)HE

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1400 uM [U-100% 13C; U-100% 15N] PulM, 50 mM Hepes, 50 mM sodium chloride, 90% H2O/10% D2O[13C, 15N] PulM 400uM in Hepes 50mM, NaCl 50mMPulM uniform labelled90% H2O/10% D2O
solution2400 uM 50% [13C, 15N] and 50% [12C, 14N] PulM, 50 mM Hepes, 50 mM sodium chloride, 90% H2O/10% D2O50%[13C, 15N] and 50%[12C, 14N] PulM 400uM in Hepes 50mM, NaCl 50mMPulM mixed labelled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMPulM[U-100% 13C; U-100% 15N]1
50 mMHepesnatural abundance1
50 mMsodium chloridenatural abundance1
400 uMPulM50% [13C, 15N] and 50% [12C, 14N]2
50 mMHepesnatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 50 mM / Label: Hepes 50mM pH7, NaCl, 50 mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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